Module atompack.bond

A dict-like abstraction for a bond between atoms.

"""A dict-like abstraction for a bond between atoms."""

from collections.abc import MutableMapping
from typing import Tuple

import orjson


class Bond(MutableMapping):
    """Dict like object containing arbitrary bond properties.
    
    Note:
        End users should not construct Bond objects directly.

    Args:
        indices: Index of each atom in the bond.
    """

    def __init__(self, indices: Tuple[int, int], **kwargs) -> None:
        self._attrs = {k: v for k, v in kwargs.items()}
        self._attrs["indices"] = indices

    ######################
    #    Constructors    #
    ######################

    @classmethod
    def from_json(cls, s: str) -> 'Bond':
        """Initializes from a JSON string."""
        # load dict from JSON string
        data = orjson.loads(s)

        # validate type
        _type = data.pop("type")
        if _type != cls.__name__:
            raise TypeError(f"cannot deserialize from type `{_type}`")

        # process indices
        indices = data.pop("indices")
        if indices is None:
            raise ValueError("`indices` is a required attribute")
        indices = (indices[0], indices[1])

        # return instance
        return cls(indices, **data)

    #######################################
    #    MutableMapping Implementation    #
    #######################################

    def __getitem__(self, key):
        return self._attrs[key]

    def __setitem__(self, key, value):
        self._attrs[key] = value

    def __delitem__(self, key):
        del self._attrs[key]

    def __iter__(self):
        return iter(self._attrs)

    def __len__(self):
        return len(self._attrs)

    ####################
    #    Properties    #
    ####################

    @property
    def indices(self) -> Tuple[int, int]:
        """Returns the index of each atom in the bond."""
        return self._attrs["indices"]

    ########################
    #    Public Methods    #
    ########################

    def to_json(self) -> str:
        """Returns the JSON serialized representation."""
        _attrs = self._attrs.copy()
        _attrs["type"] = type(self).__name__
        return orjson.dumps(_attrs, option=orjson.OPT_SERIALIZE_NUMPY)

Classes

class Bond (indices: Tuple[int, int], **kwargs)

Dict like object containing arbitrary bond properties.

Note

End users should not construct Bond objects directly.

Args

indices

Index of each atom in the bond.

Expand source code

class Bond(MutableMapping):
    """Dict like object containing arbitrary bond properties.
    
    Note:
        End users should not construct Bond objects directly.

    Args:
        indices: Index of each atom in the bond.
    """

    def __init__(self, indices: Tuple[int, int], **kwargs) -> None:
        self._attrs = {k: v for k, v in kwargs.items()}
        self._attrs["indices"] = indices

    ######################
    #    Constructors    #
    ######################

    @classmethod
    def from_json(cls, s: str) -> 'Bond':
        """Initializes from a JSON string."""
        # load dict from JSON string
        data = orjson.loads(s)

        # validate type
        _type = data.pop("type")
        if _type != cls.__name__:
            raise TypeError(f"cannot deserialize from type `{_type}`")

        # process indices
        indices = data.pop("indices")
        if indices is None:
            raise ValueError("`indices` is a required attribute")
        indices = (indices[0], indices[1])

        # return instance
        return cls(indices, **data)

    #######################################
    #    MutableMapping Implementation    #
    #######################################

    def __getitem__(self, key):
        return self._attrs[key]

    def __setitem__(self, key, value):
        self._attrs[key] = value

    def __delitem__(self, key):
        del self._attrs[key]

    def __iter__(self):
        return iter(self._attrs)

    def __len__(self):
        return len(self._attrs)

    ####################
    #    Properties    #
    ####################

    @property
    def indices(self) -> Tuple[int, int]:
        """Returns the index of each atom in the bond."""
        return self._attrs["indices"]

    ########################
    #    Public Methods    #
    ########################

    def to_json(self) -> str:
        """Returns the JSON serialized representation."""
        _attrs = self._attrs.copy()
        _attrs["type"] = type(self).__name__
        return orjson.dumps(_attrs, option=orjson.OPT_SERIALIZE_NUMPY)

Ancestors

• collections.abc.MutableMapping
• collections.abc.Mapping
• collections.abc.Collection
• collections.abc.Sized
• collections.abc.Iterable
• collections.abc.Container

Static methods

def from_json(s: str) ‑> Bond

Initializes from a JSON string.

Expand source code

@classmethod
def from_json(cls, s: str) -> 'Bond':
    """Initializes from a JSON string."""
    # load dict from JSON string
    data = orjson.loads(s)

    # validate type
    _type = data.pop("type")
    if _type != cls.__name__:
        raise TypeError(f"cannot deserialize from type `{_type}`")

    # process indices
    indices = data.pop("indices")
    if indices is None:
        raise ValueError("`indices` is a required attribute")
    indices = (indices[0], indices[1])

    # return instance
    return cls(indices, **data)

Instance variables

var indices : Tuple[int, int]

Returns the index of each atom in the bond.

Expand source code

@property
def indices(self) -> Tuple[int, int]:
    """Returns the index of each atom in the bond."""
    return self._attrs["indices"]

Methods

def to_json(self) ‑> str

Returns the JSON serialized representation.

Expand source code

def to_json(self) -> str:
    """Returns the JSON serialized representation."""
    _attrs = self._attrs.copy()
    _attrs["type"] = type(self).__name__
    return orjson.dumps(_attrs, option=orjson.OPT_SERIALIZE_NUMPY)